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首页> 外文期刊>The Journal of Antibiotics: An International Journal >Computational identification and analysis of orphan assembly-line polyketide synthases
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Computational identification and analysis of orphan assembly-line polyketide synthases

机译：孤儿流水线聚酮化合物合酶的计算鉴定和分析

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The increasing availability of DNA sequence data offers an opportunity for identifying new assembly-line polyketide synthases (PKSs) that produce biologically active natural products. We developed an automated method to extract and consolidate all multimodular PKS sequences (including hybrid PKSon-ribosomal peptide synthetases) in the National Center for Biotechnology Information (NCBI) database, generating a non-redundant catalog of 885 distinct assembly-line PKSs, the majority of which were orphans associated with no known polyketide product. Two in silico experiments highlight the value of this search method and resulting catalog. First, we identified an orphan that could be engineered to produce an analog of albocycline, an interesting antibiotic whose gene cluster has not yet been sequenced. Second, we identified and analyzed a hitherto overlooked family of metazoan multimodular PKSs, including one from Caenorhabditis elegans. We also developed a comparative analysis method that identified sequence relationships among known and orphan PKSs. As expected, PKS sequences clustered according to structural similarities between their polyketide products. The utility of this method was illustrated by highlighting an interesting orphan from the genus Burkholderia that has no close relatives. Our search method and catalog provide a community resource for the discovery of new families of assembly-line PKSs and their antibiotic products.
机译：DNA序列数据的可用性不断提高，为鉴定产生生物活性天然产物的新装配线聚酮化合物合酶（PKS）提供了机会。我们开发了一种自动方法来提取和整合国家生物技术信息中心（NCBI）数据库中的所有多模块PKS序列（包括杂化PKS /非核糖体肽合成酶），从而生成了885个不同的装配线PKS的非冗余目录，其中大多数是与未知聚酮化合物产品无关的孤儿。两次计算机模拟实验突出了这种搜索方法和生成的目录的价值。首先，我们确定了一个孤儿，可以将该孤儿改造成albocycline的类似物，albocycline是一种有趣的抗生素，其基因簇尚未进行测序。其次，我们确定并分析了一个迄今为止被忽视的后生多模块PKS家族，其中包括一个秀丽隐杆线虫。我们还开发了一种比较分析方法，可以识别已知和孤立的PKS之间的序列关系。如所期望的，PKS序列根据它们的聚酮化合物产物之间的结构相似性聚类。通过突出显示伯克霍尔德氏菌属中一个没有近亲的有趣孤儿，说明了该方法的实用性。我们的搜索方法和目录为发现装配线PKS及其抗生素产品的新家族提供了社区资源。

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